11 20-09 mbsb single molecule techniques.ppt
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This document contains over 100 images from various scientific sources related to topics in optics, microscopy, fluorescence, plasmonics, and single molecule techniques. The images depict experimental setups, microscopy images, diagrams, graphs, and other figures illustrating different scientific phenomena and techniques. Captions provide brief descriptions and citations for the source of each image.
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Bk 1997-0675%2 ech005mganguly123
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1) Polymeric excipients like PEG can stabilize proteins against denaturation during freezing by increasing the transfer free energy of the protein. However, these same polymers can induce phase separation in aqueous solutions.
2) During lyophilization, the concentrating effects of freezing can cause formulations to enter the two-phase region, resulting in liquid/liquid phase separation. This subjects the protein to potential partitioning between phases with different compositions.
3) Experimental studies on hemoglobin lyophilized in PEG/dextran mixtures provide evidence that phase separation during lyophilization can damage protein structure in the dried state.Vpdsc manual
Vpdsc manualmganguly123
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This document is the user manual for the VP-DSC MicroCalorimeter. It provides specifications for the instrument, safety information, and instructions for operation. Key details include:
- The VP-DSC allows for high sensitivity measurement of heat capacity, binding thermodynamics, and kinetics.
- Safety precautions must be followed when using hazardous or volatile solutions in the tantalum cells.
- VPViewer software interfaces with Origin for instrument control and real-time data display.
- Sections provide tutorials for common experiments, calibration procedures, troubleshooting tips, and maintenance instructions.Scan rate m ab-dsc
Scan rate m ab-dscmganguly123
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1. The study characterized the aggregation of recombinant human Interleukin-1 receptor type II (rhuIL-1RII) using differential scanning calorimetry (DSC) and size exclusion chromatography (SEC).
2. A scan-rate dependence in the DSC experiment and a break from linearity in initial aggregation rates near the melting temperature (Tm) suggested that protein unfolding significantly contributes to the aggregation reaction pathway.
3. A mechanistic model was developed to extract meaningful thermodynamic and kinetic parameters from the irreversibly denatured aggregation process by simulating how unfolding properties could predict aggregation rates at different temperatures above and below the Tm.Wei wang
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This document reviews lyophilization (freeze-drying) as a method for developing solid protein pharmaceuticals. Lyophilization generates stresses that can denature proteins, including low temperature stress, freezing stresses from increased concentration and ice formation, and drying stress from removing the hydration shell. Several studies are discussed that demonstrate denaturation of specific proteins from these stresses during lyophilization and storage. The review discusses excipient protection of proteins, lyophilization cycle design, and formulation strategies to increase stability of solid protein pharmaceuticals and overcome instability issues.Protein hydration
Protein hydrationmganguly123
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This document summarizes the calculation of translational friction and intrinsic viscosity for four globular proteins (ribonuclease A, lysozyme, myoglobin, and chymotrypsinogen A) using their detailed atomic structures. The inclusion of a 0.9 Angstrom thick hydration shell around each protein allows the calculated translational friction and intrinsic viscosity to match experimental measurements. This hydration shell thickness corresponds to a hydration level of 0.3-0.4 grams of water per gram of protein, consistent with measurements from other techniques. Using detailed protein structures thus allows hydrodynamic measurements to support a unified picture of protein hydration, in contrast to earlier models that treated proteins as ellipsoids and found widely varying hydrSalts and proteins
Salts and proteinsmganguly123
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This document summarizes a study that investigated how different salts screen charge interactions in proteins. Specifically, it examined the effects of NaCl, guanidinium chloride, and guanidinium thiocyanate on the stability of wild-type E. coli thioredoxin and a variant. The results suggest that more denaturing salts like guanidinium chloride are more efficient at screening charge interactions than NaCl. This efficiency correlates with the salts' position in the Hofmeister series and ability to accumulate on protein surfaces. An electrostatic model was used to estimate contributions of charge interactions to stability.Proton euilibria in minor groove of dna
Proton euilibria in minor groove of dnamganguly123
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1) The document describes an experiment testing the prediction that regions of increased hydrogen ion density exist in the grooves of DNA. Probes with variable linker lengths and a proton-sensitive carboxyl group were attached to DNA in the minor groove.
2) The apparent pKa values of the carboxyl groups were higher than in free solution, increasing with shorter linker lengths. This agrees with calculations showing higher hydrogen ion density in the grooves.
3) The experiment provides experimental evidence supporting the theoretical prediction of acidic domains with elevated hydrogen ion density in the DNA minor groove.Ef
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This document summarizes a study that investigated the effects of two disaccharides (trehalose and sucrose) and trimethylamine N-oxide (TMAO) on amyloid-beta (A硫) aggregation and interaction with lipid membranes. The key findings were:
1) In the absence of lipid vesicles, trehalose and sucrose delayed A硫 aggregation as measured by Thioflavin T fluorescence, but TMAO did not affect aggregation.
2) In the presence of lipid vesicles, all three osmolytes (trehalose, sucrose, TMAO) significantly attenuated dye leakage from the vesicles induced by A硫 aggregates.
3) Hydrogen exchange mass spectrometry (HX-MS) andRavi chari
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1) The study examines how long- and short-range electrostatic interactions affect the rheology and protein-protein interactions (PPI) of highly concentrated monoclonal antibody (mAb) solutions.
2) At high concentrations, both long- and short-range interactions contribute significantly to PPI, whereas at low concentrations only long-range interactions are important.
3) The study uses high frequency rheology, dynamic light scattering, circular dichroism, and zeta potential measurements to characterize PPI over a range of pH and ionic strengths, and develops a 3D computer model of the mAb to study charge distribution.Bk 1997-0675%2 ech004
Bk 1997-0675%2 ech004mganguly123
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This chapter reviews the oxidation of methionine residues in model peptides. It discusses how neighboring amino acids can influence the oxidation pattern of methionine. For example, when a hydroxyl radical attacks Thr-Met, the neighboring threonine residue is cleaved. It also notes that the oxidation of peptides and proteins is a complex process that depends on the nature of the oxidizing species and the peptide/protein sequence and structure. Oxidation can lead to chain reactions as oxidation products themselves can initiate further oxidation remote from the initial attack site.Phase diagram
Phase diagrammganguly123
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The document discusses several phase diagrams generated using different experimental data visualization techniques including:
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Bk 1994-0567%2 ech006mganguly123
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Basic fibroblast growth factor (bFGF) is being investigated for its ability to accelerate wound healing. Sulfated compounds like heparin enhance the stability of bFGF against thermal denaturation. To assess the effect on bFGF shelf life, formulations containing these excipients were incubated and analyzed. In the presence of sulfated compounds, precipitates formed that dissociated back to multimers with native structure, whereas without them precipitates were unfolded protein. Disulfide-linked multimers also increased in solution with sulfated compounds. Heparin stabilized bFGF structure and prevented rearrangement of disulfide bonds, indirectly promoting multimerization. However, loss of soluble bFGF monomer stillDs cto optimizeantibodymanuf
Ds cto optimizeantibodymanufmganguly123
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This document summarizes the use of differential scanning calorimetry (DSC) to optimize an antibody manufacturing process. DSC was used to screen conditions for a viral inactivation step and identify increased pH storage conditions for maximum stability. Low pH treatment reduced thermal stability, indicating structure loss. DSC provided insights into instability causes and process improvements, demonstrating its role in biotherapeutic development.Bk 1994-0567%2 ech016
Bk 1994-0567%2 ech016mganguly123
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This document describes a study on controlled intracranial delivery of antibodies in rats. The researchers developed polymer matrices and microspheres for long-term antibody release directly in the brain. They implanted polymer discs containing IgG antibodies in rat brains and measured IgG concentrations at the implantation site and other brain regions over 28 days, finding highest levels with the polymer implants. The polymer provided sustained antibody levels beyond what was achieved with direct injection.Dsc peptide
Dsc peptidemganguly123
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This document summarizes a study that measured the enthalpy change (H) associated with the 留-helix to random coil transition of an alanine peptide in water using calorimetry. The researchers synthesized a 50-residue peptide containing primarily alanine residues and determined its H to be between 0.9-1.3 kcal/mol per residue, providing a basic parameter for predicting thermal unfolding of peptide helices. Circular dichroism spectra and melting curves confirmed the peptide adopted an 留-helical structure at low temperatures and underwent a reversible helix-coil transition. The H value suggests the peptide backbone, rather than side chains, makes the dominant contribution to helix stability.Bk 1997-0675%2 ech003
Bk 1997-0675%2 ech003mganguly123
油
1) Aspartame degradation kinetics depend on factors like pH, temperature, buffer type and concentration, and water activity. Higher temperatures, pH, buffer concentrations and water activities increase degradation rates.
2) The activation energies for aspartame degradation decrease with increasing pH or moisture content. Phosphate buffer significantly enhances degradation more than citrate buffer.
3) In solid systems, degradation rates increase with higher initial buffer concentrations and water activities. However, the glass transition temperature does not influence degradation rates as much as water activity.Bk 1997-0675%2 ech010
Bk 1997-0675%2 ech010mganguly123
油
This chapter discusses the application of light scattering techniques to analyze the solution behavior of protein pharmaceuticals. It provides examples of using light scattering to characterize proteins and protein complexes, detect soluble aggregate formation, and elucidate protein-ligand interactions. The chapter also describes the theoretical background and instrumentation for light scattering measurements and analysis. It presents applications of light scattering including analyzing self-associating protein systems, selecting optimal solvent conditions, and studying the kinetics of molecular interactions.Ion water interaction biophysical journal
Ion water interaction biophysical journalmganguly123
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The document discusses how the charge density of ions affects their strength of hydration and interactions in biological structures. It finds that small, highly charged ions (kosmotropes) strongly bind water molecules, while large monovalent ions of low charge density (chaotropes) weakly bind water. Crystalline salts dissolve exothermically only when one ion is a kosmotrope and the other is a chaotrope. This suggests kosmotropes and chaotropes preferentially form ion pairs in solution. The major intracellular ionsphosphate and carboxylate anions and potassium/arginine cationsbehave as kosmotropes and chaotropes, respectively, allowing themProtein thermodynamics
Protein thermodynamicsmganguly123
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This document presents a study using differential scanning calorimetry (DSC) to examine the thermal stability of S-protein and its complexes with S-peptide at pH 7.0. DSC measurements showed that S-protein denatures through a reversible two-state transition with a denaturation temperature between 38.5-40.0属C and enthalpy of 165-180 kJ/mol, demonstrating its lower stability without S-peptide. A two-dimensional nonlinear regression analysis of excess heat capacity curves at varying temperatures and S-peptide concentrations was used to determine the binding thermodynamic parameters, yielding values of Kb = 1.10 106 M-1, bH = -185 kJBk 1994-0567%2 ech005
Bk 1994-0567%2 ech005mganguly123
油
The document summarizes the origin of photosensitivity in a monoclonal immunoglobulin G (IgG). UV irradiation of the monoclonal IgG causes a 70% decrease in intrinsic fluorescence and the appearance of new fluorescence, suggesting photooxidation of one or two tryptophan residues. This leads to extensive quenching of the protein's fluorescence through nonradiative energy transfer, even though few residues are directly oxidized. The photooxidation products, N-formylkynurenine and kynurenine, absorb light above 300 nm and contribute to changes in the UV-visible absorption spectrum with irradiation.More Related Content
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1) Polymeric excipients like PEG can stabilize proteins against denaturation during freezing by increasing the transfer free energy of the protein. However, these same polymers can induce phase separation in aqueous solutions.
2) During lyophilization, the concentrating effects of freezing can cause formulations to enter the two-phase region, resulting in liquid/liquid phase separation. This subjects the protein to potential partitioning between phases with different compositions.
3) Experimental studies on hemoglobin lyophilized in PEG/dextran mixtures provide evidence that phase separation during lyophilization can damage protein structure in the dried state.Vpdsc manual
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油
This document is the user manual for the VP-DSC MicroCalorimeter. It provides specifications for the instrument, safety information, and instructions for operation. Key details include:
- The VP-DSC allows for high sensitivity measurement of heat capacity, binding thermodynamics, and kinetics.
- Safety precautions must be followed when using hazardous or volatile solutions in the tantalum cells.
- VPViewer software interfaces with Origin for instrument control and real-time data display.
- Sections provide tutorials for common experiments, calibration procedures, troubleshooting tips, and maintenance instructions.Scan rate m ab-dsc
Scan rate m ab-dscmganguly123
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1. The study characterized the aggregation of recombinant human Interleukin-1 receptor type II (rhuIL-1RII) using differential scanning calorimetry (DSC) and size exclusion chromatography (SEC).
2. A scan-rate dependence in the DSC experiment and a break from linearity in initial aggregation rates near the melting temperature (Tm) suggested that protein unfolding significantly contributes to the aggregation reaction pathway.
3. A mechanistic model was developed to extract meaningful thermodynamic and kinetic parameters from the irreversibly denatured aggregation process by simulating how unfolding properties could predict aggregation rates at different temperatures above and below the Tm.Wei wang
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油
This document reviews lyophilization (freeze-drying) as a method for developing solid protein pharmaceuticals. Lyophilization generates stresses that can denature proteins, including low temperature stress, freezing stresses from increased concentration and ice formation, and drying stress from removing the hydration shell. Several studies are discussed that demonstrate denaturation of specific proteins from these stresses during lyophilization and storage. The review discusses excipient protection of proteins, lyophilization cycle design, and formulation strategies to increase stability of solid protein pharmaceuticals and overcome instability issues.Protein hydration
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油
This document summarizes the calculation of translational friction and intrinsic viscosity for four globular proteins (ribonuclease A, lysozyme, myoglobin, and chymotrypsinogen A) using their detailed atomic structures. The inclusion of a 0.9 Angstrom thick hydration shell around each protein allows the calculated translational friction and intrinsic viscosity to match experimental measurements. This hydration shell thickness corresponds to a hydration level of 0.3-0.4 grams of water per gram of protein, consistent with measurements from other techniques. Using detailed protein structures thus allows hydrodynamic measurements to support a unified picture of protein hydration, in contrast to earlier models that treated proteins as ellipsoids and found widely varying hydrSalts and proteins
Salts and proteinsmganguly123
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This document summarizes a study that investigated how different salts screen charge interactions in proteins. Specifically, it examined the effects of NaCl, guanidinium chloride, and guanidinium thiocyanate on the stability of wild-type E. coli thioredoxin and a variant. The results suggest that more denaturing salts like guanidinium chloride are more efficient at screening charge interactions than NaCl. This efficiency correlates with the salts' position in the Hofmeister series and ability to accumulate on protein surfaces. An electrostatic model was used to estimate contributions of charge interactions to stability.Proton euilibria in minor groove of dna
Proton euilibria in minor groove of dnamganguly123
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1) The document describes an experiment testing the prediction that regions of increased hydrogen ion density exist in the grooves of DNA. Probes with variable linker lengths and a proton-sensitive carboxyl group were attached to DNA in the minor groove.
2) The apparent pKa values of the carboxyl groups were higher than in free solution, increasing with shorter linker lengths. This agrees with calculations showing higher hydrogen ion density in the grooves.
3) The experiment provides experimental evidence supporting the theoretical prediction of acidic domains with elevated hydrogen ion density in the DNA minor groove.Ef
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This document summarizes a study that investigated the effects of two disaccharides (trehalose and sucrose) and trimethylamine N-oxide (TMAO) on amyloid-beta (A硫) aggregation and interaction with lipid membranes. The key findings were:
1) In the absence of lipid vesicles, trehalose and sucrose delayed A硫 aggregation as measured by Thioflavin T fluorescence, but TMAO did not affect aggregation.
2) In the presence of lipid vesicles, all three osmolytes (trehalose, sucrose, TMAO) significantly attenuated dye leakage from the vesicles induced by A硫 aggregates.
3) Hydrogen exchange mass spectrometry (HX-MS) andRavi chari
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1) The study examines how long- and short-range electrostatic interactions affect the rheology and protein-protein interactions (PPI) of highly concentrated monoclonal antibody (mAb) solutions.
2) At high concentrations, both long- and short-range interactions contribute significantly to PPI, whereas at low concentrations only long-range interactions are important.
3) The study uses high frequency rheology, dynamic light scattering, circular dichroism, and zeta potential measurements to characterize PPI over a range of pH and ionic strengths, and develops a 3D computer model of the mAb to study charge distribution.Bk 1997-0675%2 ech004
Bk 1997-0675%2 ech004mganguly123
油
This chapter reviews the oxidation of methionine residues in model peptides. It discusses how neighboring amino acids can influence the oxidation pattern of methionine. For example, when a hydroxyl radical attacks Thr-Met, the neighboring threonine residue is cleaved. It also notes that the oxidation of peptides and proteins is a complex process that depends on the nature of the oxidizing species and the peptide/protein sequence and structure. Oxidation can lead to chain reactions as oxidation products themselves can initiate further oxidation remote from the initial attack site.Phase diagram
Phase diagrammganguly123
油
The document discusses several phase diagrams generated using different experimental data visualization techniques including:
1) A phase diagram of ricin toxin A-chain created using fluorescence and circular dichroism spectroscopic data showing four protein states.
2) An empirical phase diagram of the respiratory syncytial virus determined from multiple biophysical measurements across a pH range.
3) Phase diagrams of various non-viral gene delivery vehicles and proteins mapped against pH and temperature.Bk 1994-0567%2 ech006
Bk 1994-0567%2 ech006mganguly123
油
Basic fibroblast growth factor (bFGF) is being investigated for its ability to accelerate wound healing. Sulfated compounds like heparin enhance the stability of bFGF against thermal denaturation. To assess the effect on bFGF shelf life, formulations containing these excipients were incubated and analyzed. In the presence of sulfated compounds, precipitates formed that dissociated back to multimers with native structure, whereas without them precipitates were unfolded protein. Disulfide-linked multimers also increased in solution with sulfated compounds. Heparin stabilized bFGF structure and prevented rearrangement of disulfide bonds, indirectly promoting multimerization. However, loss of soluble bFGF monomer stillDs cto optimizeantibodymanuf
Ds cto optimizeantibodymanufmganguly123
油
This document summarizes the use of differential scanning calorimetry (DSC) to optimize an antibody manufacturing process. DSC was used to screen conditions for a viral inactivation step and identify increased pH storage conditions for maximum stability. Low pH treatment reduced thermal stability, indicating structure loss. DSC provided insights into instability causes and process improvements, demonstrating its role in biotherapeutic development.Bk 1994-0567%2 ech016
Bk 1994-0567%2 ech016mganguly123
油
This document describes a study on controlled intracranial delivery of antibodies in rats. The researchers developed polymer matrices and microspheres for long-term antibody release directly in the brain. They implanted polymer discs containing IgG antibodies in rat brains and measured IgG concentrations at the implantation site and other brain regions over 28 days, finding highest levels with the polymer implants. The polymer provided sustained antibody levels beyond what was achieved with direct injection.Dsc peptide
Dsc peptidemganguly123
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This document summarizes a study that measured the enthalpy change (H) associated with the 留-helix to random coil transition of an alanine peptide in water using calorimetry. The researchers synthesized a 50-residue peptide containing primarily alanine residues and determined its H to be between 0.9-1.3 kcal/mol per residue, providing a basic parameter for predicting thermal unfolding of peptide helices. Circular dichroism spectra and melting curves confirmed the peptide adopted an 留-helical structure at low temperatures and underwent a reversible helix-coil transition. The H value suggests the peptide backbone, rather than side chains, makes the dominant contribution to helix stability.Bk 1997-0675%2 ech003
Bk 1997-0675%2 ech003mganguly123
油
1) Aspartame degradation kinetics depend on factors like pH, temperature, buffer type and concentration, and water activity. Higher temperatures, pH, buffer concentrations and water activities increase degradation rates.
2) The activation energies for aspartame degradation decrease with increasing pH or moisture content. Phosphate buffer significantly enhances degradation more than citrate buffer.
3) In solid systems, degradation rates increase with higher initial buffer concentrations and water activities. However, the glass transition temperature does not influence degradation rates as much as water activity.Bk 1997-0675%2 ech010
Bk 1997-0675%2 ech010mganguly123
油
This chapter discusses the application of light scattering techniques to analyze the solution behavior of protein pharmaceuticals. It provides examples of using light scattering to characterize proteins and protein complexes, detect soluble aggregate formation, and elucidate protein-ligand interactions. The chapter also describes the theoretical background and instrumentation for light scattering measurements and analysis. It presents applications of light scattering including analyzing self-associating protein systems, selecting optimal solvent conditions, and studying the kinetics of molecular interactions.Ion water interaction biophysical journal
Ion water interaction biophysical journalmganguly123
油
The document discusses how the charge density of ions affects their strength of hydration and interactions in biological structures. It finds that small, highly charged ions (kosmotropes) strongly bind water molecules, while large monovalent ions of low charge density (chaotropes) weakly bind water. Crystalline salts dissolve exothermically only when one ion is a kosmotrope and the other is a chaotrope. This suggests kosmotropes and chaotropes preferentially form ion pairs in solution. The major intracellular ionsphosphate and carboxylate anions and potassium/arginine cationsbehave as kosmotropes and chaotropes, respectively, allowing themProtein thermodynamics
Protein thermodynamicsmganguly123
油
This document presents a study using differential scanning calorimetry (DSC) to examine the thermal stability of S-protein and its complexes with S-peptide at pH 7.0. DSC measurements showed that S-protein denatures through a reversible two-state transition with a denaturation temperature between 38.5-40.0属C and enthalpy of 165-180 kJ/mol, demonstrating its lower stability without S-peptide. A two-dimensional nonlinear regression analysis of excess heat capacity curves at varying temperatures and S-peptide concentrations was used to determine the binding thermodynamic parameters, yielding values of Kb = 1.10 106 M-1, bH = -185 kJBk 1994-0567%2 ech005
Bk 1994-0567%2 ech005mganguly123
油
The document summarizes the origin of photosensitivity in a monoclonal immunoglobulin G (IgG). UV irradiation of the monoclonal IgG causes a 70% decrease in intrinsic fluorescence and the appearance of new fluorescence, suggesting photooxidation of one or two tryptophan residues. This leads to extensive quenching of the protein's fluorescence through nonradiative energy transfer, even though few residues are directly oxidized. The photooxidation products, N-formylkynurenine and kynurenine, absorb light above 300 nm and contribute to changes in the UV-visible absorption spectrum with irradiation.11 20-09 mbsb single molecule techniques.ppt
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